[2024-01-25 17:44:50,551] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:44:50,552] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:44:50,552] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa7748cf-1dc7-45a2-abd0-be76b9744c60/dqc_reference
[2024-01-25 17:44:51,651] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:44:51,652] [INFO] Task started: Prodigal
[2024-01-25 17:44:51,652] [INFO] Running command: gunzip -c /var/lib/cwl/stg17c736b1-bcf5-445f-a98a-14e9d4cc6982/GCF_025949695.1_ASM2594969v1_genomic.fna.gz | prodigal -d GCF_025949695.1_ASM2594969v1_genomic.fna/cds.fna -a GCF_025949695.1_ASM2594969v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:45:04,465] [INFO] Task succeeded: Prodigal
[2024-01-25 17:45:04,465] [INFO] Task started: HMMsearch
[2024-01-25 17:45:04,465] [INFO] Running command: hmmsearch --tblout GCF_025949695.1_ASM2594969v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa7748cf-1dc7-45a2-abd0-be76b9744c60/dqc_reference/reference_markers.hmm GCF_025949695.1_ASM2594969v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:45:04,817] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:45:04,818] [INFO] Found 6/6 markers.
[2024-01-25 17:45:04,865] [INFO] Query marker FASTA was written to GCF_025949695.1_ASM2594969v1_genomic.fna/markers.fasta
[2024-01-25 17:45:04,865] [INFO] Task started: Blastn
[2024-01-25 17:45:04,865] [INFO] Running command: blastn -query GCF_025949695.1_ASM2594969v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa7748cf-1dc7-45a2-abd0-be76b9744c60/dqc_reference/reference_markers.fasta -out GCF_025949695.1_ASM2594969v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:05,803] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:05,812] [INFO] Selected 15 target genomes.
[2024-01-25 17:45:05,812] [INFO] Target genome list was writen to GCF_025949695.1_ASM2594969v1_genomic.fna/target_genomes.txt
[2024-01-25 17:45:05,828] [INFO] Task started: fastANI
[2024-01-25 17:45:05,828] [INFO] Running command: fastANI --query /var/lib/cwl/stg17c736b1-bcf5-445f-a98a-14e9d4cc6982/GCF_025949695.1_ASM2594969v1_genomic.fna.gz --refList GCF_025949695.1_ASM2594969v1_genomic.fna/target_genomes.txt --output GCF_025949695.1_ASM2594969v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:45:19,353] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:19,353] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa7748cf-1dc7-45a2-abd0-be76b9744c60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:45:19,353] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa7748cf-1dc7-45a2-abd0-be76b9744c60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:45:19,363] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:45:19,363] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:45:19,363] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Pararhodobacter zhoushanensis	strain=ZQ420	GCA_003990445.1	2479545	2479545	type	True	94.0699	1424	1550	95	below_threshold
Pararhodobacter aggregans	strain=D1-19	GCA_003075525.1	404875	404875	type	True	81.7013	987	1550	95	below_threshold
Pararhodobacter aggregans	strain=DSM 18938	GCA_003054005.1	404875	404875	type	True	81.6669	978	1550	95	below_threshold
Pararhodobacter marinus	strain=CIC4N-9	GCA_003122215.1	2184063	2184063	type	True	81.3659	901	1550	95	below_threshold
Pararhodobacter oceanensis	strain=AM505	GCA_003076755.1	2172121	2172121	type	True	79.1475	661	1550	95	below_threshold
Gemmobacter nectariphilus	strain=DSM 15620	GCA_000429765.1	220343	220343	type	True	78.2391	447	1550	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	78.1544	385	1550	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	78.0401	417	1550	95	below_threshold
Allgaiera indica	strain=CGMCC 1.10859	GCA_014653075.1	765699	765699	type	True	77.9492	410	1550	95	below_threshold
Allgaiera indica	strain=DSM 24802	GCA_900106675.1	765699	765699	type	True	77.9387	413	1550	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	77.9034	387	1550	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	77.7813	388	1550	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.755	366	1550	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	77.4265	387	1550	95	below_threshold
Paracoccus yeei	strain=ATCC BAA-599	GCA_000622145.1	147645	147645	type	True	77.4159	392	1550	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:45:19,364] [INFO] DFAST Taxonomy check result was written to GCF_025949695.1_ASM2594969v1_genomic.fna/tc_result.tsv
[2024-01-25 17:45:19,365] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:45:19,365] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:45:19,365] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa7748cf-1dc7-45a2-abd0-be76b9744c60/dqc_reference/checkm_data
[2024-01-25 17:45:19,366] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:45:19,424] [INFO] Task started: CheckM
[2024-01-25 17:45:19,424] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025949695.1_ASM2594969v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025949695.1_ASM2594969v1_genomic.fna/checkm_input GCF_025949695.1_ASM2594969v1_genomic.fna/checkm_result
[2024-01-25 17:46:10,445] [INFO] Task succeeded: CheckM
[2024-01-25 17:46:10,446] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:46:10,468] [INFO] ===== Completeness check finished =====
[2024-01-25 17:46:10,469] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:46:10,470] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025949695.1_ASM2594969v1_genomic.fna/markers.fasta)
[2024-01-25 17:46:10,470] [INFO] Task started: Blastn
[2024-01-25 17:46:10,470] [INFO] Running command: blastn -query GCF_025949695.1_ASM2594969v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa7748cf-1dc7-45a2-abd0-be76b9744c60/dqc_reference/reference_markers_gtdb.fasta -out GCF_025949695.1_ASM2594969v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:12,314] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:12,319] [INFO] Selected 11 target genomes.
[2024-01-25 17:46:12,319] [INFO] Target genome list was writen to GCF_025949695.1_ASM2594969v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:46:12,333] [INFO] Task started: fastANI
[2024-01-25 17:46:12,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg17c736b1-bcf5-445f-a98a-14e9d4cc6982/GCF_025949695.1_ASM2594969v1_genomic.fna.gz --refList GCF_025949695.1_ASM2594969v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025949695.1_ASM2594969v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:46:23,011] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:23,019] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:46:23,019] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_003990445.1	s__Pararhodobacter zhoushanensis	94.0699	1424	1550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075525.1	s__Pararhodobacter aggregans	81.6908	988	1550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001691415.1	s__Pararhodobacter sp001691415	81.4659	924	1550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003122215.1	s__Pararhodobacter marinus	81.3963	897	1550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017303295.1	s__Pararhodobacter sp017303295	81.2078	910	1550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003076755.1	s__Pararhodobacter oceanensis	79.1475	661	1550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479725.1	s__Pararhodobacter sp905479725	79.0513	368	1550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314715.1	s__Pararhodobacter sp001314715	78.5224	515	1550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007131945.1	s__Pararhodobacter sp007131945	78.1647	398	1550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	99.16	99.15	0.86	0.82	3	-
GCA_903917595.1	s__Tabrizicola sp903917595	77.0928	309	1550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487335.1	s__S012-89 sp015487335	76.9435	256	1550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__S012-89	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:46:23,021] [INFO] GTDB search result was written to GCF_025949695.1_ASM2594969v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:46:23,021] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:46:23,024] [INFO] DFAST_QC result json was written to GCF_025949695.1_ASM2594969v1_genomic.fna/dqc_result.json
[2024-01-25 17:46:23,024] [INFO] DFAST_QC completed!
[2024-01-25 17:46:23,024] [INFO] Total running time: 0h1m32s